Interactions between RNA and other factors are ubiquitous in biology (Castello et al., “Insights Into RNA Biology From an Atlas of Mammalian mRNA-Binding Proteins,” Cell 149(6):1393-1406 (2012)). These interactions are postulated to play important roles in regulation of gene expression and in human disease (Lukong et al., “RNA-Binding Proteins in Human Genetic Disease,” Trends Genet. 24(8):416-425 (2008) and Estellar, M., “Non-Coding RNAs in Human Disease,” Nature Reviews Genetics 12:861-874 (2011)). Several methods have been developed to probe the scope of and characterize these interactions (Martin et al., “Systematic Reconstruction of RNA Functional Motifs With High-Throughput Micro fluidics,” Nature Methods 9:1192-1194 (2012) and Hafner et al., “Transcriptome-Wide Identification of RNA-Binding Protein and microRNA Target Sites by PAR-CLIP,” Cell 141(1):129-141 (2010)), but a direct method for their high-throughput, quantitative characterization is lacking (König et al., “Protein-RNA Interactions: New Genomic Technologies and Perspectives,” Nature Review Genetics 13:77-83 (2012)). The present invention is directed at overcoming this and other deficiencies in the art.